BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231735.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 5,296,559 number of mapped reads = 4,939,077 (93.25%) number of supplementary alignments = 35,630 (0.67%) number of secondary alignments = 0 number of mapped bases = 335,148,817 bp number of sequenced bases = 335,022,928 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 467,403 duplication rate = 4.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3019 >>>>>>> ACTG content number of A's = 89,330,091 bp (26.66%) number of C's = 61,830,941 bp (18.46%) number of T's = 97,221,529 bp (29.02%) number of G's = 86,566,289 bp (25.84%) number of N's = 74,078 bp (0.02%) GC percentage = 44.29% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 2,214,522 number of insertions = 23,342 mapped reads with insertion percentage = 0.47% number of deletions = 77,595 mapped reads with deletion percentage = 1.56% homopolymer indels = 46.61% >>>>>>> Coverage mean coverageData = 0.1083X std coverageData = 30.0757X There is a 7.62% of reference with a coverageData >= 1X There is a 1.79% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 20565654 0.08250994086791062 1.3366845928105342 chr2 243199373 31832092 0.13088887363208787 107.26291094324976 chr3 198022430 35170494 0.17760863756696654 0.5485065223935789 chr4 191154276 16437252 0.0859894549259259 0.4166379261106266 chr5 180915260 19512954 0.10785687177521674 0.4319677971147369 chr6 171115067 24690405 0.14429123883053502 0.7516131347775129 chr7 159138663 17900499 0.11248365835522948 1.809511975119668 chr8 146364022 12000867 0.08199328520775413 1.092757624269067 chr9 141213431 13002859 0.09207947790745202 0.7626738889618493 chr10 135534747 13425923 0.0990589003718729 0.7492708291599922 chr11 135006516 12914712 0.09565991614804725 0.9598098878916468 chr12 133851895 9851469 0.07359977234539712 0.38532413715841196 chr13 115169878 14574628 0.1265489575321075 0.46223565691027174 chr14 107349540 9873019 0.09197076205449972 0.5304897893276485 chr15 102531392 8090096 0.0789036005675218 0.35912866619673756 chr16 90354753 8343302 0.09233938141582879 0.4571581648366681 chr17 81195210 8884869 0.10942602402284568 0.5604989077460486 chr18 78077248 10693819 0.1369645994694895 1.4674693112448138 chr19 59128983 6774443 0.11457059899034625 0.9957532612469598 chr20 63025520 8949597 0.14199957414076075 0.5226840924636774 chr21 48129895 7894017 0.16401483942568335 0.5858064027607868 chr22 51304566 3375412 0.06579164903178403 0.32474933764024966 chrMT 16571 12084 0.729225755838513 1.1398750991469844 chrX 155270560 19567543 0.12602223499419335 0.5895535257541173 chrY 59373566 810808 0.013656043499223206 0.2298919423746705